Getting Ghost in Milwaukee Junction

This does mean that you aren't eligible for the Ghost experience bonus.

It does not mean that you aren't eligible for the Foxiest of the Hounds achievement.

Foxiest of the Hounds refers to if a guard runs up to an alarm panel and activates it, or a camera sets off an alarm, not the "alarmed" state that guards can go into.

Also, you already lost the "Ghost" bonus because someone spotted a body.

EDIT:

Alarmed occurs whenever a guard sees (or hears) something out of the ordinary. For example, a door open, a dead body, a hole in the wall that you punched out etc. This state varies. This state WILL disqualify you from receiving Ghost if someone spotted you or a body or something similar. This state WILL NOT disqualify you from receiving Ghost if someone spots a door opening, a hole in the wall or something similar. (At least I think this is how it works, I've received and not received Ghost in these ways, but I'm not 100% sure if this is exactly how it works)

Suspicious occurs whenever you're spotted by a camera or after guards have been hostile for a while and you've remained hidden for a while, they'll revert back to alarmed, and then suspicious. This state WILL NOT disqualify you from getting Ghost.

Hostile means that they're actively searching for your last seen location and occurs only if you've been spotted by a camera (for long enough) a robot or a guard. This state WILL disqualify you from getting Ghost.

To my recollection, I did get Ghost in this room. To do so, as soon as I hit the switch I activated stealth and crouch-walked into the nearest hole in the floor, where a floorboard had been removed. I hid inside this vent area until the funicular finally arrived, and then activated stealth, went into the funicular and closed it to complete the objective. No one was harmed, and nobody saw me.